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Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing #235

Merged
merged 70 commits into from
Mar 29, 2023
Merged

Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing #235

merged 70 commits into from
Mar 29, 2023

Commits on Mar 15, 2023

  1. Use BolusCutOffDelayTime for PASL data.

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    tsalo committed Mar 15, 2023
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  2. Add fix to vanilla CBF calculation.

    @tsalo
    tsalo committed Mar 15, 2023
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  3. Use nilearn for masking and unmasking.

    @tsalo
    tsalo committed Mar 15, 2023
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  4. Update misc.py

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    tsalo committed Mar 15, 2023
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  5. Update misc.py

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  6. Merge remote-tracking branch 'upstream/main' into pasl-bug

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  7. Move compute_cbf into ComputeCBF.

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    tsalo committed Mar 15, 2023
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  8. Update cbf_computation.py

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  9. Update cbf_computation.py

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  10. Update cbf_computation.py

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    tsalo committed Mar 15, 2023
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  11. Update cbf_computation.py

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    tsalo committed Mar 15, 2023
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  12. Remove logger messages.

    @tsalo
    tsalo committed Mar 15, 2023
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Commits on Mar 16, 2023

  1. Require BCOF be True for PASL across CBF methods.

    @tsalo
    tsalo committed Mar 16, 2023
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  2. Remove unused att output.

    @tsalo
    tsalo committed Mar 16, 2023
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  3. Remove unused BASIL inputs. 

    Not sure why the output filenames can be set as inputs when those inputs are never used...
    @tsalo
    tsalo committed Mar 16, 2023
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  4. Remove more inputs that are really outputs.

    @tsalo
    tsalo committed Mar 16, 2023
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  5. Update ge.py

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    tsalo committed Mar 16, 2023
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  6. Check ASLT more explicitly.

    @tsalo
    tsalo committed Mar 16, 2023
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  7. Expect a list if technique is Q2TIPS.

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    tsalo committed Mar 16, 2023
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Commits on Mar 17, 2023

  1. Remove duplicate references.

    @tsalo
    tsalo committed Mar 17, 2023
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  2. Work around nilearn-made singleton dims. 

    Nilearn's maskers add a singleton time dimension when the data are purely spatial.
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    tsalo committed Mar 17, 2023
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  3. Pin nilearn version. 

    Starting in 0.12.0, nilearn masker.transform on a 3D image will return a 1D array.
    @tsalo
    tsalo committed Mar 17, 2023
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  4. Improve comment.

    @tsalo
    tsalo committed Mar 17, 2023
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Commits on Mar 20, 2023

  1. Clean up CBF calculation.

    @tsalo
    tsalo committed Mar 20, 2023
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  2. Fix PASL CSF calculation.

    @tsalo
    tsalo committed Mar 20, 2023
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  3. Improve comments.

    @tsalo
    tsalo committed Mar 20, 2023
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  4. Improve ComputeCBF input/output names.

    @tsalo
    tsalo committed Mar 20, 2023
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  5. Improve documentation again.

    @tsalo
    tsalo committed Mar 20, 2023
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  6. Remove unnecessary fields from BibTeX entries.

    @tsalo
    tsalo committed Mar 20, 2023
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  7. Document ComputeCBF.

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    tsalo committed Mar 20, 2023
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  8. Update cbf_computation.py

    @tsalo
    tsalo committed Mar 20, 2023
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Commits on Mar 24, 2023

  1. Improve variable naming.

    @tsalo
    tsalo committed Mar 24, 2023
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  2. Change a lot of variable names.

    @tsalo
    tsalo committed Mar 24, 2023
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Commits on Mar 27, 2023

  1. Hopefully support QUIPSS and Q2TIPS.

    @tsalo
    tsalo committed Mar 27, 2023
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  2. Update.

    @tsalo
    tsalo committed Mar 27, 2023
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  3. Add a message about Q2TIPS.

    @tsalo
    tsalo committed Mar 27, 2023
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  4. Merge remote-tracking branch 'upstream/main' into pasl-bug

    @tsalo
    tsalo committed Mar 27, 2023
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  5. Add a test for ComputeCBF.

    @tsalo
    tsalo committed Mar 27, 2023
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  6. Update test_interfaces_cbf_computation.py

    @tsalo
    tsalo committed Mar 27, 2023
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  7. Update test_interfaces_cbf_computation.py

    @tsalo
    tsalo committed Mar 27, 2023
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  8. Just use tmpdir.

    @tsalo
    tsalo committed Mar 27, 2023
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  9. Update test_interfaces_cbf_computation.py

    @tsalo
    tsalo committed Mar 27, 2023
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  10. Add CASL labeling efficiency value.

    @tsalo
    tsalo committed Mar 27, 2023
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  11. Replace T1blood formula with hardcoded values.

    @tsalo
    tsalo committed Mar 27, 2023
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  12. Drop check within pcasl_or_pasl. Checked elsewhere.

    @tsalo
    tsalo committed Mar 27, 2023
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Commits on Mar 28, 2023

  1. Push T1blood change to another PR.

    @tsalo
    tsalo committed Mar 28, 2023
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  2. Modify PLDs in metadata during deltam selection.

    @tsalo
    tsalo committed Mar 28, 2023
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  3. Try fixing the PLDs.

    @tsalo
    tsalo committed Mar 28, 2023
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  4. Add logger messages.

    @tsalo
    tsalo committed Mar 28, 2023
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  5. Update cbf_computation.py

    @tsalo
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  6. Update cbf_computation.py

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  7. Update cbf_computation.py

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  8. Update cbf_computation.py

    @tsalo
    tsalo committed Mar 28, 2023
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  9. Fix?

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    tsalo committed Mar 28, 2023
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  10. Add another integration test.

    @tsalo
    tsalo committed Mar 28, 2023
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  11. Update test.

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  12. Skip new test for now.

    @tsalo
    tsalo committed Mar 28, 2023
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  13. Try to simplify the CBF workflows.

    @tsalo
    tsalo committed Mar 28, 2023
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  14. Fix bugs hopefully.

    @tsalo
    tsalo committed Mar 28, 2023
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  15. Move connections around a bit.

    @tsalo
    tsalo committed Mar 28, 2023
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  16. Fix bug maybe.

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    tsalo committed Mar 28, 2023
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  17. Expect failures on multi-PLD data.

    @tsalo
    tsalo committed Mar 28, 2023
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  18. Fix test.

    @tsalo
    tsalo committed Mar 28, 2023
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  19. Fix things more.

    @tsalo
    tsalo committed Mar 28, 2023
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  20. Update cbf_computation.py

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    tsalo committed Mar 28, 2023
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  21. Fix...

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    tsalo committed Mar 28, 2023
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Commits on Mar 29, 2023

  1. Update cbf_computation.py

    @tsalo
    tsalo committed Mar 29, 2023
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  2. Use first BolusCutOffDelayTime for Q2TIPS w BASIL.

    @tsalo
    tsalo committed Mar 29, 2023
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  3. Split things up a bit.

    @tsalo
    tsalo committed Mar 29, 2023
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  4. Disable Q2TIPS.

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    tsalo committed Mar 29, 2023
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